brandon,
Are you using a Durso or Hofer type device on the outlet from the overflow box? I suspect that if you can prevent a hard siphon on the outlet you could avoid pulling bubbles into the u-tube. On my overflow, I adjust the outlet so that the water level on the inside box is just below the notches. This reduces bubble formation since the water does not fall as far and those that do form are farther away from the inlet of the u-tube.
Todd